Variant report

Variant	rs55678388
Chromosome Location	chr3:158435286-158435287
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158362537..158364690-chr3:158433408..158437608,3	K562	blood:
2	chr3:158421107..158423161-chr3:158433354..158436179,2	K562	blood:
3	chr3:158433592..158436389-chr3:158442916..158446023,3	MCF-7	breast:
4	chr3:158435127..158437978-chr3:158439840..158441916,2	MCF-7	breast:
5	chr3:158430342..158432825-chr3:158434955..158438595,5	K562	blood:
6	chr3:158429563..158432825-chr3:158433996..158437681,6	K562	blood:

Variant related genes	Relation type
ENSG00000168827	Chromatin interaction

Extended variants
information (count: 77 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12489730	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12491877	0.95[ASN][1000 genomes]
rs12495962	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs12497488	0.97[ASN][1000 genomes]
rs1430413	0.97[ASN][1000 genomes]
rs1430414	0.97[ASN][1000 genomes]
rs1560417	0.97[ASN][1000 genomes]
rs1560418	0.97[ASN][1000 genomes]
rs16829365	0.90[ASN][1000 genomes]
rs17642769	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643171	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17643252	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643483	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643581	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17643860	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17643917	0.90[ASN][1000 genomes]
rs17698494	0.80[EUR][1000 genomes]
rs17699103	0.82[EUR][1000 genomes]
rs17699324	0.84[EUR][1000 genomes]
rs17699478	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17699526	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17699997	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17700122	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17700475	0.97[ASN][1000 genomes]
rs2279561	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2279562	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2307064	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2566347	0.97[ASN][1000 genomes]
rs34690420	0.97[ASN][1000 genomes]
rs3863076	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs3867391	0.83[EUR][1000 genomes]
rs55705231	0.95[ASN][1000 genomes]
rs55717824	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55776609	0.90[ASN][1000 genomes]
rs56023805	0.97[ASN][1000 genomes]
rs56078503	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56105525	0.97[ASN][1000 genomes]
rs56152025	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56235582	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56261306	0.97[ASN][1000 genomes]
rs56318834	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57262841	0.97[ASN][1000 genomes]
rs59163359	0.97[ASN][1000 genomes]
rs59173444	0.90[ASN][1000 genomes]
rs60203196	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61138408	0.97[ASN][1000 genomes]
rs61794798	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794799	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61794818	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794821	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61794822	0.97[ASN][1000 genomes]
rs61794833	0.97[ASN][1000 genomes]
rs61794834	0.97[ASN][1000 genomes]
rs61794835	0.92[ASN][1000 genomes]
rs61794858	0.97[ASN][1000 genomes]
rs61794859	0.97[ASN][1000 genomes]
rs61796760	0.82[ASN][1000 genomes]
rs61796762	0.97[ASN][1000 genomes]
rs61796764	0.95[ASN][1000 genomes]
rs61796766	0.80[ASN][1000 genomes]
rs61796768	0.95[ASN][1000 genomes]
rs61796770	0.95[ASN][1000 genomes]
rs6441221	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6761989	0.97[ASN][1000 genomes]
rs6783610	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6792908	0.97[ASN][1000 genomes]
rs73158361	0.95[ASN][1000 genomes]
rs7610009	0.83[EUR][1000 genomes]
rs7624420	0.88[ASN][1000 genomes]
rs7624702	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs55678388	GFM1	cis	Artery Tibial	GTEx
rs55678388	GFM1	cis	Nerve Tibial	GTEx
rs55678388	GFM1	cis	Esophagus Mucosa	GTEx
rs55678388	GFM1	cis	Thyroid	GTEx
rs55678388	GFM1	cis	Muscle Skeletal	GTEx
rs55678388	GFM1	Cis_1M	lymphoblastoid	RTeQTL
rs55678388	LXN	Cis_1M	lymphoblastoid	RTeQTL
rs55678388	LXN	cis	multi-tissue	Pritchard

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158390800-158444200	Weak transcription	Gastric	stomach
2	chr3:158390800-158445400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:158391000-158438800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr3:158397000-158443400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:158397000-158448000	Weak transcription	Thymus	Thymus
6	chr3:158399600-158445400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:158403600-158438600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:158408400-158443000	Weak transcription	HepG2	liver
9	chr3:158409800-158439000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr3:158411600-158439400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr3:158412200-158440800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:158412400-158439200	Weak transcription	Fetal Kidney	kidney
13	chr3:158415000-158440800	Weak transcription	Colonic Mucosa	Colon
14	chr3:158417600-158440600	Weak transcription	Aorta	Aorta
15	chr3:158421800-158435600	Strong transcription	Fetal Intestine Small	intestine
16	chr3:158423800-158438800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr3:158424200-158446000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:158426600-158436600	Strong transcription	Fetal Stomach	stomach
19	chr3:158427200-158435600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr3:158427600-158439000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr3:158427600-158440600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr3:158427800-158440400	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr3:158427800-158440600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:158427800-158440800	Weak transcription	Liver	Liver
25	chr3:158427800-158440800	Weak transcription	Esophagus	oesophagus
26	chr3:158428000-158438800	Weak transcription	Fetal Brain Female	brain
27	chr3:158428600-158438800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr3:158429000-158440600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:158429200-158438200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr3:158429400-158436200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:158429400-158438200	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:158429600-158449000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:158429800-158440800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:158430600-158435400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:158430600-158440800	Weak transcription	Small Intestine	intestine
36	chr3:158431000-158436200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr3:158431000-158438800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:158431000-158439600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr3:158431000-158439800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:158431000-158440600	Weak transcription	Fetal Thymus	thymus
41	chr3:158431000-158442000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:158431000-158442400	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:158431000-158444200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:158431000-158445400	Weak transcription	GM12878-XiMat	blood
45	chr3:158431000-158449200	Weak transcription	Brain Germinal Matrix	brain
46	chr3:158431200-158439000	Weak transcription	Primary T cells from cord blood	blood
47	chr3:158431200-158445400	Weak transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:158431200-158445800	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr3:158431400-158436000	Enhancers	A549	lung
50	chr3:158431400-158436000	Weak transcription	NHDF-Ad	bronchial

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